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Status |
Public on Apr 17, 2024 |
Title |
ChIP against H3K27me3 in E18.5 mouse male urogenital sinus replicate 1 |
Sample type |
SRA |
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Source name |
urogenital sinus
|
Organism |
Mus musculus |
Characteristics |
tissue: urogenital sinus Sex: male Stage: E18.5 antibody: H3K27me3 (Merck Millipore, 07–449) genotype: wild type strain: B6CBAF1
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Male and female UGS were isolated separately and placed into 1x PBS containing 10% FCS on ice. ChIP-seq experiments were performed as previously described in (10.1101/gad.281055.116). Briefly, they were fixed for 10 mn in 1% formaldehyde at room temperature and the crosslinking reaction was quenched with glycine. Subsequently, nuclei were extracted and chromatin was sheared using a water-bath sonicator (Covaris E220 evolution ultra-sonicator). Immunoprecipitation was done using the following anti- H3K27ac (Abcam, ab4729) or anti-H3K27me3 (Merck Millipore, 07–449). Libraries were prepared using the TruSeq protocol, and sequenced on the Illumina HiSeq system (100 bp single-end reads) according to manufactures instructions.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
All scripts necessary to reproduce the analyses are available at https://github.com/AurelieHintermann/HintermannBoltEtAl2024. Raw ChIP-seq single-reads were processed with CutAdapt version 4.1 (-a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC for single-reads and -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15) to remove Truseq or Nextera adapters and bad quality bases. Filtered reads were mapped on mm39 with bowtie2 version 2.4.5 with the default parameters. Only alignments with a mapping quality above 30 were kept (Samtools v1.16.1). Peaks were called and coverage was generated by MACS2 version 2.2.7.1 with with --call-summits -B (and --nomodel --extsize 200 for single-read). Coverages were normalized to million mapped reads/pairs. Assembly: mm39 Supplementary files format and content: *narrowPeak.gz: peaks from MACS2 Supplementary files format and content: *bw: coverage from MACS2 normalized to million mapped reads
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Submission date |
Dec 15, 2023 |
Last update date |
Apr 17, 2024 |
Contact name |
Aurelie Hintermann |
E-mail(s) |
aur.hin@gmail.com
|
Organization name |
University of Geneva
|
Department |
Genetics and Evolution
|
Street address |
30 quai Ernest-Ansermet
|
City |
Geneva |
ZIP/Postal code |
1205 |
Country |
Switzerland |
|
|
Platform ID |
GPL21103 |
Series (2) |
GSE250267 |
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS |
GSE250367 |
EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE WITH THE EMERGENCE OF DIGITS AND GENITALS [ChIP-seq] |
|
Relations |
BioSample |
SAMN38859256 |
SRA |
SRX22906488 |